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- PDB-8ibo: Crystal structure of Wild-Type Mycobacterium tuberculosis ClpC1 N... -

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Basic information

Entry
Database: PDB / ID: 8ibo
TitleCrystal structure of Wild-Type Mycobacterium tuberculosis ClpC1 N-terminal domain in complex with Lassomycin
Components
  • Lassomycin
  • Negative regulator of genetic competence ClpC/mecB
KeywordsCHAPERONE
Function / homology
Function and homology information


cellular response to heat / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Clp amino terminal domain, pathogenicity island component / Clp, repeat (R) domain / Clp repeat (R) domain profile. / : / Clp, N-terminal domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / Negative regulator of genetic competence ClpC/mecB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Lentzea kentuckyensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsJagdev, M.K. / Vasudevan, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Crystal structure of the N-terminal domain of MtClpC1 in complex with the anti-mycobacterial natural peptide Lassomycin.
Authors: Jagdev, M.K. / Tompa, D.R. / Ling, L.L. / Peoples, A.J. / Dandapat, J. / Mohapatra, C. / Lewis, K. / Vasudevan, D.
History
DepositionFeb 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1May 8, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Negative regulator of genetic competence ClpC/mecB
C: Lassomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7154
Polymers17,5972
Non-polymers1182
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-10 kcal/mol
Surface area7890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.431, 58.468, 64.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Negative regulator of genetic competence ClpC/mecB


Mass: 15695.099 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: clpC_1 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A655JDN0
#2: Protein/peptide Lassomycin


Mass: 1902.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lentzea kentuckyensis (bacteria)
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.4 M sodium acetate, 0.1 M sodium cacodylate (pH 6.5)

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Data collection

DiffractionMean temperature: 103 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.83→36.86 Å / Num. obs: 16474 / % possible obs: 100 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 30.4
Reflection shellResolution: 1.83→1.87 Å / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 4 / Num. unique obs: 1650

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→36.86 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.308 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 821 5 %RANDOM
Rwork0.183 ---
obs0.185 15605 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.99 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å20 Å20 Å2
2---1.18 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.83→36.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 0 8 57 1301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0181308
X-RAY DIFFRACTIONr_bond_other_d0.0010.021306
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9171762
X-RAY DIFFRACTIONr_angle_other_deg1.2262.9323002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4415167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73422.62361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78115244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8361516
X-RAY DIFFRACTIONr_chiral_restr0.0970.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021470
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02270
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8772.032652
X-RAY DIFFRACTIONr_mcbond_other3.8322.025649
X-RAY DIFFRACTIONr_mcangle_it4.8673.008817
X-RAY DIFFRACTIONr_mcangle_other4.8643.008818
X-RAY DIFFRACTIONr_scbond_it5.3232.608656
X-RAY DIFFRACTIONr_scbond_other5.3192.613657
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2473.71944
X-RAY DIFFRACTIONr_long_range_B_refined9.15226.0041482
X-RAY DIFFRACTIONr_long_range_B_other9.15725.8231473
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.83→1.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 68 -
Rwork0.242 1110 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.834-0.3458-0.67474.4189-0.0172.96540.1294-0.0250.0280.1952-0.1104-0.0825-0.32240.1559-0.01910.0718-0.02770.01170.01380.00290.0241-17.476-5.70810.872
211.21830.30531.42785.5916-2.38398.79550.0363-0.20270.09190.11110.23820.3876-0.4283-0.5133-0.27450.05750.0062-0.04110.0470.03540.1472-32.381-14.6054.769
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 142
2X-RAY DIFFRACTION2C1 - 15

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